Starting phenix.real_space_refine on Thu Jul 2 11:43:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ew1_31344/07_2026/7ew1_31344.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ew1_31344/07_2026/7ew1_31344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ew1_31344/07_2026/7ew1_31344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ew1_31344/07_2026/7ew1_31344.map" model { file = "/net/cci-nas-00/data/ceres_data/7ew1_31344/07_2026/7ew1_31344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ew1_31344/07_2026/7ew1_31344.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 61 5.16 5 C 5550 2.51 5 N 1492 2.21 5 O 1629 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8735 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 474 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "D" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1832 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 1998 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'J8C': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7954 SG CYS A 197 54.361 65.194 28.586 1.00145.71 S Time building chain proxies: 2.06, per 1000 atoms: 0.24 Number of scatterers: 8735 At special positions: 0 Unit cell: (92.65, 124.95, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 F 3 9.00 O 1629 8.00 N 1492 7.00 C 5550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 182 " distance=1.48 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 282 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 544.4 milliseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 33.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 1 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.861A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 22 removed outlier: 3.926A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.873A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 9 through 23 removed outlier: 3.585A pdb=" N SER D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.669A pdb=" N GLU D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 211 through 216 removed outlier: 3.587A pdb=" N CYS D 214 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 215 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU D 216 " --> pdb=" O HIS D 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 211 through 216' Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.660A pdb=" N SER D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 281 Processing helix chain 'D' and resid 295 through 309 removed outlier: 3.507A pdb=" N ALA D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 300 " --> pdb=" O TYR D 296 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 352 removed outlier: 4.186A pdb=" N VAL D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.588A pdb=" N TYR A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 63 removed outlier: 4.715A pdb=" N VAL A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N CYS A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 96 Processing helix chain 'A' and resid 104 through 139 removed outlier: 4.198A pdb=" N TRP A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 166 removed outlier: 3.702A pdb=" N LEU A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 190 through 223 removed outlier: 3.824A pdb=" N VAL A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 247 through 275 removed outlier: 3.781A pdb=" N VAL A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Proline residue: A 266 - end of helix removed outlier: 3.921A pdb=" N VAL A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 removed outlier: 3.963A pdb=" N ALA A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 4.391A pdb=" N THR A 309 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.858A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.900A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.616A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.399A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.864A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 208 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.709A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 243 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 188 through 190 removed outlier: 7.474A pdb=" N LYS D 35 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ILE D 222 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU D 37 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N CYS D 224 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU D 39 " --> pdb=" O CYS D 224 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.060A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.177A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR E 243 " --> pdb=" O TYR E 227 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2834 1.34 - 1.46: 1948 1.46 - 1.58: 4035 1.58 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 8903 Sorted by residual: bond pdb=" C07 J8C A 401 " pdb=" C09 J8C A 401 " ideal model delta sigma weight residual 1.481 1.539 -0.058 2.00e-02 2.50e+03 8.36e+00 bond pdb=" N10 J8C A 401 " pdb=" O11 J8C A 401 " ideal model delta sigma weight residual 1.362 1.413 -0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" C32 J8C A 401 " pdb=" C33 J8C A 401 " ideal model delta sigma weight residual 1.536 1.490 0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" C33 J8C A 401 " pdb=" C34 J8C A 401 " ideal model delta sigma weight residual 1.533 1.488 0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" CA VAL A 185 " pdb=" CB VAL A 185 " ideal model delta sigma weight residual 1.540 1.568 -0.028 1.36e-02 5.41e+03 4.11e+00 ... (remaining 8898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11749 1.79 - 3.59: 261 3.59 - 5.38: 41 5.38 - 7.17: 8 7.17 - 8.97: 5 Bond angle restraints: 12064 Sorted by residual: angle pdb=" N VAL A 145 " pdb=" CA VAL A 145 " pdb=" C VAL A 145 " ideal model delta sigma weight residual 107.28 114.98 -7.70 1.59e+00 3.96e-01 2.35e+01 angle pdb=" N LEU A 135 " pdb=" CA LEU A 135 " pdb=" C LEU A 135 " ideal model delta sigma weight residual 111.28 116.24 -4.96 1.09e+00 8.42e-01 2.07e+01 angle pdb=" O GLY A 265 " pdb=" C GLY A 265 " pdb=" N PRO A 266 " ideal model delta sigma weight residual 121.07 122.57 -1.50 3.60e-01 7.72e+00 1.73e+01 angle pdb=" N VAL A 16 " pdb=" CA VAL A 16 " pdb=" C VAL A 16 " ideal model delta sigma weight residual 110.62 114.84 -4.22 1.02e+00 9.61e-01 1.71e+01 angle pdb=" N ALA A 143 " pdb=" CA ALA A 143 " pdb=" C ALA A 143 " ideal model delta sigma weight residual 109.81 118.35 -8.54 2.21e+00 2.05e-01 1.49e+01 ... (remaining 12059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 5018 23.08 - 46.16: 277 46.16 - 69.25: 21 69.25 - 92.33: 9 92.33 - 115.41: 6 Dihedral angle restraints: 5331 sinusoidal: 2075 harmonic: 3256 Sorted by residual: dihedral pdb=" C VAL A 185 " pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" CB VAL A 185 " ideal model delta harmonic sigma weight residual -122.00 -141.09 19.09 0 2.50e+00 1.60e-01 5.83e+01 dihedral pdb=" N VAL A 185 " pdb=" C VAL A 185 " pdb=" CA VAL A 185 " pdb=" CB VAL A 185 " ideal model delta harmonic sigma weight residual 123.40 140.52 -17.12 0 2.50e+00 1.60e-01 4.69e+01 dihedral pdb=" C20 J8C A 401 " pdb=" C19 J8C A 401 " pdb=" C24 J8C A 401 " pdb=" C23 J8C A 401 " ideal model delta sinusoidal sigma weight residual -56.35 59.06 -115.41 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 5328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.097: 1386 1.097 - 2.194: 0 2.194 - 3.291: 0 3.291 - 4.387: 0 4.387 - 5.484: 2 Chirality restraints: 1388 Sorted by residual: chirality pdb=" C33 J8C A 401 " pdb=" C32 J8C A 401 " pdb=" C34 J8C A 401 " pdb=" C35 J8C A 401 " both_signs ideal model delta sigma weight residual False 2.65 -2.84 5.48 2.00e-01 2.50e+01 7.52e+02 chirality pdb=" C19 J8C A 401 " pdb=" C16 J8C A 401 " pdb=" C20 J8C A 401 " pdb=" C24 J8C A 401 " both_signs ideal model delta sigma weight residual False -2.57 2.69 -5.26 2.00e-01 2.50e+01 6.92e+02 chirality pdb=" CA VAL A 185 " pdb=" N VAL A 185 " pdb=" C VAL A 185 " pdb=" CB VAL A 185 " both_signs ideal model delta sigma weight residual False 2.44 1.83 0.61 2.00e-01 2.50e+01 9.29e+00 ... (remaining 1385 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO E 75 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 97 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 98 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 104 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO A 105 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " -0.016 5.00e-02 4.00e+02 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 17 2.26 - 2.92: 3591 2.92 - 3.58: 11847 3.58 - 4.24: 18607 4.24 - 4.90: 32146 Nonbonded interactions: 66208 Sorted by model distance: nonbonded pdb=" CD1 LEU A 17 " pdb=" CB LEU A 179 " model vdw 1.601 3.860 nonbonded pdb=" NE1 TRP A 264 " pdb=" ND2 ASN A 298 " model vdw 1.621 3.200 nonbonded pdb=" CE1 HIS A 18 " pdb=" SG CYS A 182 " model vdw 1.679 3.620 nonbonded pdb=" OG SER A 183 " pdb=" C ALA A 190 " model vdw 1.686 3.270 nonbonded pdb=" O HIS A 68 " pdb=" NH2 ARG A 148 " model vdw 1.783 3.120 ... (remaining 66203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.170 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.553 8906 Z= 0.337 Angle : 0.745 25.982 12070 Z= 0.429 Chirality : 0.209 5.484 1388 Planarity : 0.003 0.046 1524 Dihedral : 14.544 115.409 3222 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.52 % Favored : 97.39 % Rotamer: Outliers : 0.32 % Allowed : 5.97 % Favored : 93.71 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.24), residues: 1109 helix: 0.38 (0.29), residues: 341 sheet: -1.74 (0.28), residues: 279 loop : -2.47 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.006 0.001 TYR B 59 PHE 0.011 0.001 PHE E 80 TRP 0.013 0.001 TRP B 332 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.17 ( 8903) covalent geometry : angle 0.67945 / 0.40 (12064) SS BOND : bond 0.31920 / 17.73 ( 3) SS BOND : angle 13.74081 / 7.61 ( 6) hydrogen bonds : bond 0.19523 / 13.04 ( 364) hydrogen bonds : angle 5.64483 / 4.01 ( 1047) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8235 (ptpp) REVERT: D 209 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8780 (ttpp) REVERT: D 242 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7943 (mtp85) REVERT: D 272 ASP cc_start: 0.7805 (p0) cc_final: 0.7133 (p0) REVERT: E 73 ASP cc_start: 0.7971 (t70) cc_final: 0.7682 (t70) REVERT: E 219 LEU cc_start: 0.7996 (tt) cc_final: 0.7761 (tt) REVERT: A 131 LEU cc_start: 0.7589 (tp) cc_final: 0.7370 (tp) outliers start: 3 outliers final: 0 residues processed: 161 average time/residue: 0.1050 time to fit residues: 22.5911 Evaluate side-chains 127 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN B 44 GLN B 340 ASN C 24 ASN D 52 GLN D 255 ASN D 331 ASN E 82 GLN E 113 GLN E 194 ASN A 18 HIS ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.176862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118731 restraints weight = 11853.061| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.74 r_work: 0.3207 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8906 Z= 0.117 Angle : 0.596 8.391 12070 Z= 0.293 Chirality : 0.042 0.296 1388 Planarity : 0.004 0.053 1524 Dihedral : 6.666 64.956 1259 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.71 % Allowed : 11.41 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.25), residues: 1109 helix: 1.03 (0.28), residues: 359 sheet: -1.32 (0.29), residues: 278 loop : -2.18 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 87 TYR 0.021 0.001 TYR B 59 PHE 0.016 0.001 PHE A 268 TRP 0.006 0.001 TRP B 82 HIS 0.009 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 8903) covalent geometry : angle 0.59561 / 0.29 (12064) SS BOND : bond 0.00372 / 0.23 ( 3) SS BOND : angle 1.17815 / 0.60 ( 6) hydrogen bonds : bond 0.04382 / 3.03 ( 364) hydrogen bonds : angle 4.27962 / 3.06 ( 1047) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8294 (ptpp) REVERT: D 209 LYS cc_start: 0.9163 (ttpt) cc_final: 0.8875 (ttpp) REVERT: D 242 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7852 (mtp85) REVERT: D 276 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: E 73 ASP cc_start: 0.8023 (t70) cc_final: 0.7676 (t0) REVERT: A 131 LEU cc_start: 0.7739 (tp) cc_final: 0.7470 (tp) REVERT: A 193 TYR cc_start: 0.7769 (t80) cc_final: 0.7344 (t80) outliers start: 16 outliers final: 10 residues processed: 146 average time/residue: 0.0989 time to fit residues: 19.7395 Evaluate side-chains 136 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 292 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 69 optimal weight: 0.0000 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82 GLN E 231 GLN A 298 ASN A 302 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.177321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122055 restraints weight = 11769.394| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.94 r_work: 0.3247 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8906 Z= 0.098 Angle : 0.529 7.706 12070 Z= 0.264 Chirality : 0.040 0.220 1388 Planarity : 0.003 0.053 1524 Dihedral : 5.115 42.965 1259 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.24 % Allowed : 14.50 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.25), residues: 1109 helix: 1.25 (0.29), residues: 359 sheet: -1.01 (0.30), residues: 282 loop : -1.90 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 87 TYR 0.019 0.001 TYR A 216 PHE 0.010 0.001 PHE A 72 TRP 0.008 0.001 TRP A 264 HIS 0.002 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 8903) covalent geometry : angle 0.52856 / 0.26 (12064) SS BOND : bond 0.00364 / 0.23 ( 3) SS BOND : angle 0.68830 / 0.38 ( 6) hydrogen bonds : bond 0.03518 / 2.43 ( 364) hydrogen bonds : angle 3.99923 / 2.86 ( 1047) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8508 (ptpp) cc_final: 0.8249 (ptpp) REVERT: B 291 ASP cc_start: 0.7928 (t0) cc_final: 0.7646 (t0) REVERT: D 209 LYS cc_start: 0.9184 (ttpt) cc_final: 0.8879 (ttpp) REVERT: D 242 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7876 (mtp85) REVERT: D 276 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: E 43 LYS cc_start: 0.7846 (mmtm) cc_final: 0.7599 (mmtm) REVERT: E 73 ASP cc_start: 0.8091 (t70) cc_final: 0.7720 (t0) REVERT: A 131 LEU cc_start: 0.7905 (tp) cc_final: 0.7595 (tp) REVERT: A 193 TYR cc_start: 0.7842 (t80) cc_final: 0.7387 (t80) outliers start: 21 outliers final: 12 residues processed: 143 average time/residue: 0.0978 time to fit residues: 19.2662 Evaluate side-chains 136 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 351 CYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.178177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124331 restraints weight = 11901.567| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.73 r_work: 0.3259 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8906 Z= 0.094 Angle : 0.517 7.622 12070 Z= 0.258 Chirality : 0.040 0.197 1388 Planarity : 0.003 0.052 1524 Dihedral : 4.395 40.376 1259 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.45 % Allowed : 16.31 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.26), residues: 1109 helix: 1.44 (0.29), residues: 359 sheet: -0.73 (0.30), residues: 278 loop : -1.79 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 87 TYR 0.013 0.001 TYR D 296 PHE 0.009 0.001 PHE A 72 TRP 0.016 0.001 TRP A 264 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 ( 8903) covalent geometry : angle 0.51657 / 0.26 (12064) SS BOND : bond 0.00380 / 0.23 ( 3) SS BOND : angle 0.59013 / 0.34 ( 6) hydrogen bonds : bond 0.03175 / 2.18 ( 364) hydrogen bonds : angle 3.83769 / 2.73 ( 1047) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8526 (ptpp) cc_final: 0.8263 (ptpp) REVERT: B 291 ASP cc_start: 0.7936 (t0) cc_final: 0.7613 (t0) REVERT: D 276 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: E 73 ASP cc_start: 0.8062 (t70) cc_final: 0.7651 (t0) REVERT: A 131 LEU cc_start: 0.7938 (tp) cc_final: 0.7639 (tp) REVERT: A 137 MET cc_start: 0.8747 (mmm) cc_final: 0.8535 (tpt) REVERT: A 193 TYR cc_start: 0.7786 (t80) cc_final: 0.7421 (t80) REVERT: A 292 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6836 (tt) outliers start: 23 outliers final: 16 residues processed: 143 average time/residue: 0.0959 time to fit residues: 19.1553 Evaluate side-chains 143 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 101 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN B 237 ASN B 239 ASN E 82 GLN E 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.170974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116752 restraints weight = 11794.446| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.67 r_work: 0.3129 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8906 Z= 0.169 Angle : 0.586 7.916 12070 Z= 0.294 Chirality : 0.042 0.199 1388 Planarity : 0.003 0.053 1524 Dihedral : 4.440 37.828 1259 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.77 % Allowed : 16.63 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 1109 helix: 1.36 (0.29), residues: 364 sheet: -0.89 (0.29), residues: 289 loop : -1.71 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 87 TYR 0.019 0.002 TYR A 216 PHE 0.014 0.002 PHE B 241 TRP 0.013 0.001 TRP A 264 HIS 0.006 0.002 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 8903) covalent geometry : angle 0.58596 / 0.29 (12064) SS BOND : bond 0.00514 / 0.31 ( 3) SS BOND : angle 0.52167 / 0.30 ( 6) hydrogen bonds : bond 0.03836 / 2.62 ( 364) hydrogen bonds : angle 4.01974 / 2.88 ( 1047) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8570 (ptpp) cc_final: 0.8288 (ptpp) REVERT: B 291 ASP cc_start: 0.8001 (t0) cc_final: 0.7716 (t0) REVERT: D 198 MET cc_start: 0.8470 (ttp) cc_final: 0.8232 (tpp) REVERT: E 43 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7812 (mmtm) REVERT: E 73 ASP cc_start: 0.7997 (t70) cc_final: 0.7610 (t0) REVERT: A 71 MET cc_start: 0.4168 (ttp) cc_final: 0.3460 (mmm) REVERT: A 131 LEU cc_start: 0.7901 (tp) cc_final: 0.7605 (tp) REVERT: A 193 TYR cc_start: 0.7771 (t80) cc_final: 0.7427 (t80) REVERT: A 218 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 292 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6999 (tt) outliers start: 26 outliers final: 19 residues processed: 143 average time/residue: 0.1028 time to fit residues: 20.0855 Evaluate side-chains 142 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.169847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111054 restraints weight = 11801.135| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.53 r_work: 0.3091 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8906 Z= 0.193 Angle : 0.622 8.172 12070 Z= 0.312 Chirality : 0.043 0.208 1388 Planarity : 0.004 0.053 1524 Dihedral : 4.604 38.338 1259 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.88 % Allowed : 18.44 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.25), residues: 1109 helix: 1.36 (0.29), residues: 364 sheet: -0.83 (0.29), residues: 294 loop : -1.75 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 87 TYR 0.024 0.002 TYR B 59 PHE 0.014 0.002 PHE B 241 TRP 0.014 0.002 TRP A 264 HIS 0.007 0.002 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 ( 8903) covalent geometry : angle 0.62157 / 0.31 (12064) SS BOND : bond 0.00613 / 0.37 ( 3) SS BOND : angle 0.53251 / 0.31 ( 6) hydrogen bonds : bond 0.04089 / 2.79 ( 364) hydrogen bonds : angle 4.13365 / 2.97 ( 1047) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8297 (ptpp) REVERT: B 217 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7781 (ptt) REVERT: B 291 ASP cc_start: 0.8249 (t0) cc_final: 0.7943 (t0) REVERT: E 6 GLU cc_start: 0.8216 (pm20) cc_final: 0.7934 (pm20) REVERT: E 43 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7745 (mmtm) REVERT: E 73 ASP cc_start: 0.8083 (t70) cc_final: 0.7670 (t0) REVERT: E 183 GLN cc_start: 0.8332 (pm20) cc_final: 0.8040 (pm20) REVERT: A 71 MET cc_start: 0.4302 (ttp) cc_final: 0.3481 (mmm) REVERT: A 131 LEU cc_start: 0.7979 (tp) cc_final: 0.7682 (tp) REVERT: A 193 TYR cc_start: 0.7746 (t80) cc_final: 0.7442 (t80) REVERT: A 218 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 261 VAL cc_start: 0.8490 (t) cc_final: 0.8126 (m) REVERT: A 292 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.7011 (tt) outliers start: 27 outliers final: 22 residues processed: 135 average time/residue: 0.1002 time to fit residues: 18.6720 Evaluate side-chains 138 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 109 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN E 82 GLN E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115842 restraints weight = 11813.416| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.61 r_work: 0.3174 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8906 Z= 0.095 Angle : 0.539 9.881 12070 Z= 0.266 Chirality : 0.040 0.208 1388 Planarity : 0.003 0.054 1524 Dihedral : 4.257 39.403 1259 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.24 % Allowed : 18.98 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.26), residues: 1109 helix: 1.58 (0.29), residues: 365 sheet: -0.67 (0.30), residues: 294 loop : -1.58 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.024 0.001 TYR A 216 PHE 0.009 0.001 PHE D 189 TRP 0.014 0.001 TRP A 264 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 8903) covalent geometry : angle 0.53873 / 0.27 (12064) SS BOND : bond 0.00360 / 0.22 ( 3) SS BOND : angle 0.50515 / 0.31 ( 6) hydrogen bonds : bond 0.03114 / 2.13 ( 364) hydrogen bonds : angle 3.88492 / 2.78 ( 1047) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8561 (ptpp) cc_final: 0.8332 (ptpp) REVERT: B 291 ASP cc_start: 0.8257 (t0) cc_final: 0.7905 (t0) REVERT: E 43 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7735 (mmtm) REVERT: E 73 ASP cc_start: 0.8000 (t70) cc_final: 0.7568 (t0) REVERT: A 71 MET cc_start: 0.4109 (ttp) cc_final: 0.3282 (mmm) REVERT: A 131 LEU cc_start: 0.7973 (tp) cc_final: 0.7655 (tp) REVERT: A 193 TYR cc_start: 0.7769 (t80) cc_final: 0.7510 (t80) REVERT: A 218 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 261 VAL cc_start: 0.8433 (t) cc_final: 0.8089 (m) REVERT: A 292 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6960 (tt) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 0.0905 time to fit residues: 17.0958 Evaluate side-chains 133 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 0.0170 chunk 107 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.172913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113819 restraints weight = 11729.684| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.69 r_work: 0.3152 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8906 Z= 0.123 Angle : 0.571 8.473 12070 Z= 0.282 Chirality : 0.041 0.215 1388 Planarity : 0.003 0.055 1524 Dihedral : 4.269 38.467 1259 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.35 % Allowed : 19.19 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.26), residues: 1109 helix: 1.65 (0.29), residues: 365 sheet: -0.62 (0.30), residues: 288 loop : -1.59 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.013 0.001 TYR B 59 PHE 0.011 0.001 PHE B 241 TRP 0.014 0.001 TRP A 264 HIS 0.004 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8903) covalent geometry : angle 0.57032 / 0.28 (12064) SS BOND : bond 0.00536 / 0.32 ( 3) SS BOND : angle 1.63601 / 1.11 ( 6) hydrogen bonds : bond 0.03406 / 2.31 ( 364) hydrogen bonds : angle 3.89945 / 2.79 ( 1047) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.329 Fit side-chains REVERT: B 15 LYS cc_start: 0.8543 (ptpp) cc_final: 0.8289 (ptpp) REVERT: B 291 ASP cc_start: 0.8093 (t0) cc_final: 0.7732 (t0) REVERT: E 73 ASP cc_start: 0.7827 (t70) cc_final: 0.7480 (t0) REVERT: E 149 VAL cc_start: 0.8692 (p) cc_final: 0.8288 (m) REVERT: E 183 GLN cc_start: 0.8209 (pm20) cc_final: 0.7978 (pm20) REVERT: A 71 MET cc_start: 0.4229 (ttp) cc_final: 0.3406 (mmm) REVERT: A 131 LEU cc_start: 0.7850 (tp) cc_final: 0.7546 (tp) REVERT: A 137 MET cc_start: 0.8785 (mmm) cc_final: 0.8228 (tpt) REVERT: A 193 TYR cc_start: 0.7736 (t80) cc_final: 0.7481 (t80) REVERT: A 215 ILE cc_start: 0.7578 (tt) cc_final: 0.7322 (tt) REVERT: A 218 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 261 VAL cc_start: 0.8458 (t) cc_final: 0.8101 (m) REVERT: A 292 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7086 (tt) outliers start: 22 outliers final: 16 residues processed: 137 average time/residue: 0.0816 time to fit residues: 15.6548 Evaluate side-chains 140 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.0170 chunk 72 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 30.0000 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN E 3 GLN E 82 GLN E 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.175439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122368 restraints weight = 11721.241| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.68 r_work: 0.3235 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8906 Z= 0.095 Angle : 0.546 8.233 12070 Z= 0.269 Chirality : 0.040 0.224 1388 Planarity : 0.003 0.054 1524 Dihedral : 4.162 39.559 1259 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.71 % Allowed : 19.40 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 1109 helix: 1.78 (0.29), residues: 365 sheet: -0.47 (0.30), residues: 286 loop : -1.53 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.019 0.001 TYR A 216 PHE 0.009 0.001 PHE D 189 TRP 0.014 0.001 TRP A 264 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 8903) covalent geometry : angle 0.54580 / 0.27 (12064) SS BOND : bond 0.00373 / 0.23 ( 3) SS BOND : angle 1.09114 / 0.72 ( 6) hydrogen bonds : bond 0.02970 / 2.03 ( 364) hydrogen bonds : angle 3.76754 / 2.69 ( 1047) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.320 Fit side-chains REVERT: B 291 ASP cc_start: 0.8194 (t0) cc_final: 0.7825 (t0) REVERT: C 9 ILE cc_start: 0.7487 (mp) cc_final: 0.6969 (mm) REVERT: E 73 ASP cc_start: 0.7808 (t70) cc_final: 0.7470 (t0) REVERT: E 149 VAL cc_start: 0.8619 (p) cc_final: 0.8194 (m) REVERT: E 183 GLN cc_start: 0.8193 (pm20) cc_final: 0.7943 (pm20) REVERT: A 71 MET cc_start: 0.4242 (ttp) cc_final: 0.3408 (mmm) REVERT: A 131 LEU cc_start: 0.7918 (tp) cc_final: 0.7616 (tp) REVERT: A 137 MET cc_start: 0.8772 (mmm) cc_final: 0.8215 (tpt) REVERT: A 152 LEU cc_start: 0.5941 (mm) cc_final: 0.5677 (tt) REVERT: A 193 TYR cc_start: 0.7740 (t80) cc_final: 0.7510 (t80) REVERT: A 218 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 261 VAL cc_start: 0.8424 (t) cc_final: 0.8074 (m) REVERT: A 292 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7027 (tt) outliers start: 16 outliers final: 12 residues processed: 138 average time/residue: 0.0893 time to fit residues: 17.2574 Evaluate side-chains 135 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 10 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN E 3 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.173902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119795 restraints weight = 11796.252| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.69 r_work: 0.3213 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8906 Z= 0.116 Angle : 0.569 8.078 12070 Z= 0.282 Chirality : 0.041 0.231 1388 Planarity : 0.003 0.054 1524 Dihedral : 4.148 39.181 1259 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.39 % Allowed : 20.15 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 1109 helix: 1.78 (0.29), residues: 361 sheet: -0.46 (0.31), residues: 286 loop : -1.52 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.015 0.001 TYR D 296 PHE 0.010 0.001 PHE B 241 TRP 0.028 0.001 TRP A 264 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8903) covalent geometry : angle 0.56862 / 0.28 (12064) SS BOND : bond 0.00524 / 0.32 ( 3) SS BOND : angle 0.77008 / 0.50 ( 6) hydrogen bonds : bond 0.03182 / 2.16 ( 364) hydrogen bonds : angle 3.78518 / 2.71 ( 1047) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.360 Fit side-chains REVERT: B 291 ASP cc_start: 0.8226 (t0) cc_final: 0.7858 (t0) REVERT: C 9 ILE cc_start: 0.7482 (mp) cc_final: 0.6987 (mm) REVERT: E 73 ASP cc_start: 0.7819 (t70) cc_final: 0.7469 (t0) REVERT: E 149 VAL cc_start: 0.8631 (p) cc_final: 0.8209 (m) REVERT: E 183 GLN cc_start: 0.8260 (pm20) cc_final: 0.7970 (pm20) REVERT: A 71 MET cc_start: 0.4214 (ttp) cc_final: 0.3390 (mmm) REVERT: A 131 LEU cc_start: 0.7934 (tp) cc_final: 0.7642 (tp) REVERT: A 137 MET cc_start: 0.8760 (mmm) cc_final: 0.8214 (tpt) REVERT: A 152 LEU cc_start: 0.5978 (mm) cc_final: 0.5680 (tt) REVERT: A 218 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 261 VAL cc_start: 0.8409 (t) cc_final: 0.8067 (m) REVERT: A 292 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6978 (tt) outliers start: 13 outliers final: 10 residues processed: 135 average time/residue: 0.0832 time to fit residues: 15.7859 Evaluate side-chains 134 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN E 3 GLN E 82 GLN E 231 GLN A 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122657 restraints weight = 11719.495| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.68 r_work: 0.3230 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8906 Z= 0.095 Angle : 0.553 7.992 12070 Z= 0.274 Chirality : 0.041 0.242 1388 Planarity : 0.003 0.053 1524 Dihedral : 4.084 40.549 1259 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.34 % Favored : 97.57 % Rotamer: Outliers : 1.60 % Allowed : 19.72 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1109 helix: 1.82 (0.29), residues: 365 sheet: -0.37 (0.31), residues: 286 loop : -1.46 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.022 0.001 TYR A 193 PHE 0.009 0.001 PHE D 189 TRP 0.019 0.001 TRP A 264 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 8903) covalent geometry : angle 0.55330 / 0.27 (12064) SS BOND : bond 0.00387 / 0.23 ( 3) SS BOND : angle 0.69448 / 0.44 ( 6) hydrogen bonds : bond 0.02964 / 2.01 ( 364) hydrogen bonds : angle 3.72882 / 2.67 ( 1047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.52 seconds wall clock time: 44 minutes 12.78 seconds (2652.78 seconds total)